Week 2: DNA Read, Write, and Edit
Context
This page captures my Week 2 assignment for HTGAA 2025, reformatted for Hugo. Yellow callouts mark assignment prompts; red callouts (if any) would mark AI-assisted notes.
SynBio Read/Write/Edit — Homework
Warning
About your documentation
Document every step of your in-silico and lab work. Include sketches, screenshots, notes, and even failures (plus how you fixed them).
Part 0 — Basics of Gel Electrophoresis
- Watch the lecture and recitation videos for this week.
- Optional: Review BioBootCamp (DNA “reading & editing”) overview video.
Part 1 — Benchling & In-silico Gel Art
Follow the protocol and create an in-silico gel using a reference DNA (lambda).
Protocol & tools
- Protocol (Google Doc): Gel Art: Restriction Digests and Gel Electrophoresis
https://docs.google.com/document/d/1TTZiQ79mN4w9euS2bycKIc9f0U0BC7MuvJ7_hW_7qcg/edit - Benchling (create a free account): https://benchling.com/
- Reference DNA (lambda):
- NEB product page: https://www.neb.com/products/n3011-lambda-dna
- SnapGene lambda sequence/map: https://www.snapgene.com/plasmids/basic_cloning_vectors/lambda
- GenBank entry (J02459): https://www.genome.jp/dbget-bin/www_bget?genbank-phg%3AJ02459=
Steps
Get the lambda sequence / file
- Use one of the references above to obtain the sequence (e.g., the SnapGene page).
- Example (searching for lambda sequence):
- Example (downloading a sequence/plasmid file):
Add lambda DNA to Benchling
- Import the FASTA/GenBank/SnapGene file into a new Benchling project (or paste the sequence).
- Confirm length and cohesive ends are recognized (if provided by the source).
Plan restriction digests
- Choose enzymes that generate a distinctive band pattern for your gel “art”.
- Record enzyme names, buffers, incubation plan, and expected fragment sizes.
Simulate and export
- Simulate the digest and generate expected band sizes.
- Save screenshots of your enzyme map and gel preview.
Design your gel art
- Arrange lanes to create a pattern or message.
- Add a ladder lane and any controls you need.
Tip
Deliverables for Part 1
- Short write-up of your design idea.
- Enzyme list + expected fragment sizes.
- Screenshots: annotated sequence map and gel preview.
- Notes on what worked/didn’t (troubleshooting).
Submission checklist
- Overview paragraph explaining the intent of the gel art.
- Sources cited for the lambda sequence.
- Benchling screenshots (sequence map with restriction sites, gel preview).
- Parameters: enzymes, buffer, temperature, time, and expected band sizes.
- Reflection: mistakes, fixes, and next steps.